Public health problems in armed conflicts have been well documented, however, effective national health policies and international assistance strategies in transition periods from conflict to peace have not been well established. After the long lasted conflicts in Sri Lanka, the Government and the rebel LTTE signed a cease-fire agreement in February 2002. As the peace negotiation has been disrupted since April 2003, a long-term prospect for peace is yet uncertain at present. The objective of this research is to detect unmet needs in health services in Northern Province in Sri Lanka, and to recommend fair and effective health strategies for post-conflict reconstruction. First, we compared a 20-year trend of health services and health status between the post-conflict Northern Province and other areas not directly affected by conflict in Sri Lanka by analyzing data published by Sri Lankan government and other agencies. Then, we conducted open-ended self-administered questionnaires to health care providers and inhabitants in Northern Province, and key informant interviews in Northern Province and other areas. The major health problems in Northern Province were high maternal mortality, significant shortage of human resources for health (HRH), and inadequate water and sanitation systems. Poor access to health facilities, lack of basic health knowledge, insufficient health awareness programs for inhabitants, and mental health problems among communities were pointed by the questionnaire respondents. Shortage of HRH and people’s negligence for health were perceived as the major obstacles to improving the current health situation in Northern Province. The key informant interviews revealed that Sri Lankan HRH outside Northern Province had only limited information about the health issues in Northern Province. It is required to develop and allocate HRH strategically for the effective reconstruction of health service systems in Northern Province. The empowerment of inhabitants and communities through health awareness programs and the development of a systematic mental health strategy at the state level are also important. It is necessary to provide with the objective information of gaps in health indicators by region for promoting mutual understanding between Tamil and Sinhalese. International assistance should be provided not only for the post-conflict area but also for other underprivileged areas to avoid unnecessary grievance.